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discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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Escherichia coli K-12 substr. MG1655 Enzyme: RPnTP hydrolase



Gene: phnM Accession Numbers: EG10722 (EcoCyc), b4095, ECK4088

Regulation Summary Diagram: ?

Summary:
PhnM catalyzes hydrolysis of α-D-ribose-1-methylphosphonate-5-triphosphate, generating α-D-ribose-1-methylphosphonate 5-phosphate and pyrophosphate [Kamat11]. PhnM is a member of the amidohydrolase superfamily [Seibert05].

phnM is part of an operon that is phosphate starvation-inducible and required for use of phosphonate and phosphite as phosphorous sources [Yakovleva98, Metcalf91, Chen90]. PhnM appeared to be required for carbon-phosphorous lyase activity [Metcalf93].

Gene Citations: [Wanner92]

Locations: cytosol, inner membrane

Map Position: [4,314,105 <- 4,315,241] (92.98 centisomes)
Length: 1137 bp / 378 aa

Molecular Weight of Polypeptide: 42.01 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013419 , CGSC:34526 , EchoBASE:EB0716 , EcoGene:EG10722 , EcoliWiki:b4095 , ModBase:P16689 , OU-Microarray:b4095 , PortEco:phnM , Protein Model Portal:P16689 , RefSeq:NP_418519 , RegulonDB:EG10722 , SMR:P16689 , String:511145.b4095 , UniProt:P16689

Relationship Links: InterPro:IN-FAMILY:IPR011059 , InterPro:IN-FAMILY:IPR012696 , Pfam:IN-FAMILY:PF01979

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0019700 - organic phosphonate catabolic process Inferred from experiment Inferred by computational analysis [GOA01, Metcalf93]
Molecular Function: GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005886 - plasma membrane

MultiFun Terms: cell structure membrane
metabolism metabolism of other compounds phosphorous metabolism

Essentiality data for phnM knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Last-Curated ? 22-Nov-2011 by Keseler I , SRI International


Enzymatic reaction of: RPnTP hydrolase

EC Number: 3.6.1.63

α-D-ribose-1-methylphosphonate-5-triphosphate + H2O <=> α-D-ribose-1-methylphosphonate 5-phosphate + diphosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates for α-D-ribose-1-methylphosphonate-5-triphosphate: ribose triphosphate [Kamat11 ]

In Pathways: methylphosphonate degradation I

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
α-D-ribose-1-methylphosphonate-5-triphosphate
56.0
6.4
[Kamat11]


Sequence Features

Feature Class Location Citations Comment
Extrinsic-Sequence-Variant 318
[UniProt10a]
Alternate sequence: Q → E; UniProt: (in strain: B);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4095 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10722; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Chen90: Chen CM, Ye QZ, Zhu ZM, Wanner BL, Walsh CT (1990). "Molecular biology of carbon-phosphorus bond cleavage. Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B." J Biol Chem 265(8);4461-71. PMID: 2155230

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kamat11: Kamat SS, Williams HJ, Raushel FM (2011). "Intermediates in the transformation of phosphonates to phosphate by bacteria." Nature 480(7378);570-3. PMID: 22089136

Metcalf91: Metcalf WW, Wanner BL (1991). "Involvement of the Escherichia coli phn (psiD) gene cluster in assimilation of phosphorus in the form of phosphonates, phosphite, Pi esters, and Pi." J Bacteriol 1991;173(2);587-600. PMID: 1846145

Metcalf93: Metcalf WW, Wanner BL (1993). "Mutational analysis of an Escherichia coli fourteen-gene operon for phosphonate degradation, using TnphoA' elements." J Bacteriol 175(11);3430-42. PMID: 8388873

Seibert05: Seibert CM, Raushel FM (2005). "Structural and catalytic diversity within the amidohydrolase superfamily." Biochemistry 44(17);6383-91. PMID: 15850372

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wanner92: Wanner BL, Metcalf WW (1992). "Molecular genetic studies of a 10.9-kb operon in Escherichia coli for phosphonate uptake and biodegradation." FEMS Microbiol Lett 79(1-3);133-9. PMID: 1335942

Yakovleva98: Yakovleva GM, Kim SK, Wanner BL (1998). "Phosphate-independent expression of the carbon-phosphorus lyase activity of Escherichia coli." Appl Microbiol Biotechnol 49(5);573-8. PMID: 9650256

Other References Related to Gene Regulation

Jiang95: Jiang W, Metcalf WW, Lee KS, Wanner BL (1995). "Molecular cloning, mapping, and regulation of Pho regulon genes for phosphonate breakdown by the phosphonatase pathway of Salmonella typhimurium LT2." J Bacteriol 1995;177(22);6411-21. PMID: 7592415

Makino91: Makino K, Kim SK, Shinagawa H, Amemura M, Nakata A (1991). "Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12." J Bacteriol 1991;173(8);2665-12. PMID: 1840580

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

Wanner90: Wanner BL, Boline JA (1990). "Mapping and molecular cloning of the phn (psiD) locus for phosphonate utilization in Escherichia coli." J Bacteriol 172(3);1186-96. PMID: 2155195

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, BIOCYC13A.